Chem3D Users Manual - CambridgeSoft

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Administrator 238• Keyboard Modifiers CambridgeSoft
Appendix F: 2D to 3D Conversion Overview This section discusses how Chem3D performs the conversion from two to three dimensions when opening a ChemDraw or ISIS/Draw document, when pasting a ChemDraw or ISIS/Draw structure from the Clipboard, or when opening a ChemDraw connection table file. While Chem3D can read in and assimilate any ChemDraw structure, you can assist Chem3D in the two- to three-dimensional conversion of your models by following the suggestions in this Appendix. Chem3D uses the atom labels and bonds drawn in ChemDraw to form the structure of your model. For every bond drawn in ChemDraw, a corresponding bond is created in Chem3D. Every atom label is converted into at least one atom. Dative bonds are converted to single bonds with a positive formal charge added to one atom (the atom at the tail of the dative bond) and a negative formal charge added to the other (the head of the dative bond). + - S O Stereochemical Relationships Chem3D uses the stereo bonds and H-Dot and H-Dash atom labels in a ChemDraw structure to define the stereochemical relationships in the corresponding model. Wedged bonds in ChemDraw indicate a bond where the atom at the wide end of the bond is in front of the atom at the narrow end of the bond. Wedged hashed bonds indicate the opposite: the atom at the wide end of a wedged hashed bond is behind the atom at the other end of the bond. Example 1 In Example 1, the two phenyl rings are trans about the cyclopentane ring. The phenyl ring on the left is attached by a wedged hashed bond; the phenyl ring on the right is attached by a wedged bond. You can also use dashed, hashed, and bold bonds. However, you should be aware of potential ambiguity where these non-directional bonds are used. A dashed, hashed, or bold bond must be between one atom that has at least three attachments and one atom that has no more than two attachments, including the dashed, hashed, or bold bond. Example 2 NH 2 In Example 2, the nitrogen atom is placed behind the ring system and the two methyl groups are placed in front of the ring system. Each of these three atoms is bonded to only one other atom, so they are presumed to be at the wide ends of the stereo bonds. Appendices ChemOffice 2005/Appendix 2D to 3D Conversion • 239 Stereochemical Relationships
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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Administrator In the Measurements t
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Administrator Tutorial 7: Docking M
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Administrator atoms are relatively
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator VDW Interactions The
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Administrator Editing Parameters Yo
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Administrator Adding Parameters to
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Administrator Rectification, when d
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Administrator Translucent surface t
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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